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Last change on this file was 14507, checked in by westram, 8 years ago
merge enabled gcc-versions from 'trunk' into 'stable' compiled, ran unit tests and did a quick feature check for each gcc enabled skipped gcc 4.7.4 (interferes with my perl version, but should work) adds: log:trunk@13120,13359,13759,13928,14037
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 65.5 KB

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1	# =============================================================== #
2	# #
3	# File : Makefile #
4	# #
5	# Institute of Microbiology (Technical University Munich) #
6	# http://www.arb-home.de/ #
7	# #
8	# =============================================================== #
9
10	# -----------------------------------------------------
11	# The ARB Makefile is aware of the following defines:
12	#
13	# CC C compiler (should be defined by OS)
14	# CXX C++ compiler (should be defined by OS)
15	#
16	# BUILDHOST_64=0/1 1=>compile on 64 bit platform (defaults to ARB_64)
17	# DEVELOPER=name special compilation (values: ANY,RELEASE,your name)
18	# OPENGL=0/1 whether OPENGL is available
19	#
20	# -----------------------------------------------------
21	# ARB Makefile and ARB source code are aware of the following defines:
22	#
23	# $(MACH) name of the machine (LINUX or DARWIN; see config.makefile)
24	# DEBUG compiles the DEBUG sections
25	# DEBUG_GRAPHICS all X-graphics are flushed immediately (for debugging)
26	# ARB_64=0/1 1=>compile 64 bit version
27	# UNIT_TESTS=0/1 1=>compile in unit tests and call them after build
28	# COVERAGE=0/1/2 compile in gcov support (useful together with UNIT_TESTS=1)
29	# 0=no, 1+2=compile in, 1=show
30	# STABS=0/1 force stabs format? (0 = "use default format")
31	#
32	# -----------------------------------------------------
33	# The ARB source code is aware of the following defines:
34	#
35	# NDEBUG doesn't compile the DEBUG sections
36	# DEVEL_$(DEVELOPER) developer-dependent flag (enables you to have private sections in code)
37	# DEVELOPER='ANY' (default setting) will be ignored
38	# configurable in config.makefile
39	#
40	# -----------------------------------------------------
41	# Read configuration
42	include config.makefile
43
44	# set defaults for variables commented out in config.makefile:
45	ifndef DARWIN
46	DARWIN:=0
47	endif
48	ifndef LINUX
49	LINUX:=0
50	endif
51	ifndef DEBIAN
52	DEBIAN:=0
53	endif
54	ifndef REDHAT
55	REDHAT:=0
56	endif
57	ifndef ARB_64
58	ARB_64=1#default to 64bit
59	endif
60
61	# compiler settings:
62	ifneq ($(CC),use__A_CC__instead_of__CC)
63
64	A_CC:=$(CC)# compile C
65	A_CXX:=$(CXX)# compile C++
66
67	# uncomment to ensure no submakefile uses CC and CXX directly
68	override CC:=use__A_CC__instead_of__CC
69	override CXX:=use__A_CXX__instead_of__CXX
70
71	endif
72
73	export CC CXX A_CC A_CXX
74
75	ifeq ($(LD_LIBRARY_PATH),'')
76	LD_LIBRARY_PATH:=${ARBHOME}/lib
77	endif
78
79	ifeq ($(DARWIN),1)
80	LD_LIBRARY_PATH:=${ARBHOME}/lib
81	endif
82
83	FORCEMASK = umask 002
84	NODIR=--no-print-directory
85
86	SED:=$(ARBHOME)/SH/arb_sed
87	READLINK:=$(ARBHOME)/SH/arb_readlink
88
89	# ---------------------- compiler version detection
90
91	# supported gcc versions:
92	ALLOWED_gcc_VERSIONS=\
93	4.3.1 4.3.2 4.3.3 4.3.4 \
94	4.4.1 4.4.3 4.4.5 4.4.6 4.4.7 \
95	4.5.2 \
96	4.6.1 4.6.2 4.6.3 \
97	4.7.1 4.7.2 4.7.3 \
98	4.8.0 4.8.1 4.8.2 4.8.3 4.8.4 4.8.5 \
99	4.9.0 4.9.1 4.9.2 4.9.3 \
100	5.1.0 5.2.0 \
101
102
103	# supported clang versions:
104	ALLOWED_clang_VERSIONS=\
105	4.2.1 \
106
107	# ----------------------
108
109	COMPILER_INFO:=$(shell SOURCE_TOOLS/arb_compiler_version.pl $(A_CXX))
110	COMPILER_NAME:=$(word 1,$(COMPILER_INFO))
111	COMPILER_VERSION:=$(word 2,$(COMPILER_INFO))
112
113	USE_CLANG:=0
114	ifneq ($(COMPILER_NAME),gcc)
115	ifeq ($(COMPILER_NAME),clang)
116	USE_CLANG:=1
117	else
118	$(error failed to detect COMPILER_NAME (got '$(COMPILER_NAME)', expected 'clang' or 'gcc'))
119	endif
120	endif
121
122	ifeq ($(USE_CLANG),1)
123	ALLOWED_COMPILER_VERSIONS=$(ALLOWED_clang_VERSIONS)
124	else
125	ALLOWED_COMPILER_VERSIONS=$(ALLOWED_gcc_VERSIONS)
126	endif
127
128	COMPILER_VERSION_ALLOWED=$(strip $(subst ___,,$(foreach version,$(ALLOWED_COMPILER_VERSIONS),$(findstring ___$(version)___,___$(COMPILER_VERSION)___))))
129
130	#---------------------- split gcc version
131
132	SPLITTED_VERSION:=$(subst ., ,$(COMPILER_VERSION))
133
134	USE_GCC_MAJOR:=$(word 1,$(SPLITTED_VERSION))
135	USE_GCC_MINOR:=$(word 2,$(SPLITTED_VERSION))
136	USE_GCC_PATCHLEVEL:=$(word 3,$(SPLITTED_VERSION))
137
138	USE_GCC_452_OR_HIGHER:=
139	USE_GCC_47_OR_HIGHER:=
140	USE_GCC_48_OR_HIGHER:=
141
142	ifeq ($(USE_GCC_MAJOR),4)
143	ifeq ($(USE_GCC_MINOR),5)
144	ifneq ('$(findstring $(USE_GCC_PATCHLEVEL),23456789)','')
145	USE_GCC_452_OR_HIGHER:=yes
146	endif
147	else
148	ifneq ('$(findstring $(USE_GCC_MINOR),6789)','')
149	USE_GCC_452_OR_HIGHER:=yes
150	ifneq ($(USE_GCC_MINOR),6)
151	USE_GCC_47_OR_HIGHER:=yes
152	ifneq ($(USE_GCC_MINOR),7)
153	USE_GCC_48_OR_HIGHER:=yes
154	endif
155	endif
156	endif
157	endif
158	else
159	USE_GCC_452_OR_HIGHER:=yes
160	USE_GCC_47_OR_HIGHER:=yes
161	USE_GCC_48_OR_HIGHER:=yes
162	endif
163
164	#---------------------- define special directories for non standard builds
165
166	ifeq ($(DARWIN),1)
167	OSX_FW:=/System/Library/Frameworks
168	OSX_FW_OPENGL:=$(OSX_FW)/OpenGL.framework/Versions/A/Libraries
169	OSX_FW_GLUT:=$(OSX_FW)/GLUT.framework/Versions/A/Libraries
170	OSX_FW_IMAGEIO:=$(OSX_FW)/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources
171	endif
172
173	#----------------------
174
175	ifeq ($(DARWIN),1)
176	LINK_STATIC=1# link static
177	else
178	LINK_STATIC=0# link dynamically
179	# LINK_STATIC=1# link static (testing only)
180	endif
181
182	shared_cflags :=# flags for shared lib compilation
183	lflags :=# linker flags
184	clflags :=# linker flags (when passed through gcc)
185	extended_warnings :=# warning flags for C and C++-compiler
186	extended_cpp_warnings :=# warning flags for C++-compiler only
187
188
189	ifeq ($(DEBUG),0)
190	dflags := -DNDEBUG# defines
191	ifeq ($(USE_CLANG),1)
192	cflags := -O3# compiler flags (C and C++)
193	else
194	cflags := -O4# compiler flags (C and C++)
195	lflags += -O2# linker flags
196	clflags += -Wl,-O2# passthrough linker flags
197	endif
198	endif
199
200	ifeq ($(DEBIAN),1)
201	lflags += -rpath=/usr/lib/arb/lib -z relro
202	clflags += -Wl,-rpath=/usr/lib/arb/lib -Wl,-z,relro
203	endif
204
205	ifeq ($(DEBUG),1)
206	dflags := -DDEBUG
207
208	gdb_common := -g -g3 -ggdb -ggdb3
209
210	ifeq ($(STABS),1)
211	cflags := -O0 $(gdb_common) -gstabs+ # using stabs+ (enable this for bigger debug session: debugs inlines, quick var inspect, BUT valgrind stops working :/)
212	else
213	cflags := -O0 $(gdb_common) # (using dwarf - cant debug inlines here, incredible slow on showing variable content)
214	endif
215
216	# cflags := -O0 $(gdb_common) -gdwarf-3 # (specify explicit dwarf format)
217	# cflags := -O0 $(gdb_common) -gstabs # using stabs (same here IIRC)
218	# cflags := -O2 $(gdb_common) # use this for callgrind (force inlining)
219
220	ifeq ($(DARWIN),0)
221	lflags += -g
222	clflags += -Wl,-g
223	endif
224
225	# control how much you get spammed
226	# (please do not change default in SVN, use developer specific setting as below)
227	POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl
228	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --original# dont modify compiler output
229	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --hide-Noncopyable-advices
230	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --show-useless-Weff++
231	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --no-warnings
232	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --only-first-error
233	# POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --no-warnings --only-first-error
234	ifeq ($(DEVELOPER),ELMAR)
235	POST_COMPILE := 2>&1 \| $(ARBHOME)/SOURCE_TOOLS/postcompile.pl --only-first-error
236	endif
237
238
239	# Enable extra warnings
240	extended_warnings :=
241	extended_cpp_warnings :=
242
243	# C and C++
244	extended_warnings += -Wwrite-strings -Wunused -Wno-aggregate-return -Wshadow
245
246	# C++ only
247	extended_cpp_warnings += -Wnon-virtual-dtor -Wreorder -Wpointer-arith -Wdisabled-optimization -Wmissing-format-attribute
248	extended_cpp_warnings += -Wctor-dtor-privacy# < gcc 3
249	# extended_cpp_warnings += -Wfloat-equal# gcc 3.0
250
251	# ------- above only warnings available in 3.0
252
253	ifneq ('$(COMPILER_VERSION)','4.7.3') # g++ crashes on GenomeImport.cxx when -Weffc++ is active (bug reported)
254	extended_cpp_warnings += -Weffc++# gcc 3.0.1
255	endif
256	extended_cpp_warnings += -Wmissing-noreturn# gcc 3.0.2
257	# extended_cpp_warnings += -Wold-style-cast# gcc 3.0.4 (warn about 28405 old-style casts)
258	extended_cpp_warnings += -Winit-self# gcc 3.4.0
259	extended_cpp_warnings += -Wstrict-aliasing# gcc 3.4
260	extended_cpp_warnings += -Wextra# gcc 3.4.0
261	ifeq ('$(USE_GCC_452_OR_HIGHER)','yes')
262	extended_cpp_warnings += -Wlogical-op# gcc 4.5.2
263	endif
264
265	ifeq ($(DEBUG_GRAPHICS),1)
266	dflags += -DDEBUG_GRAPHICS
267	endif
268	endif
269
270	#---------------------- turn off clang bogus warnings
271
272	ifeq ($(USE_CLANG),1)
273	# -Wmismatched-tags warns about struct/class mismatch in forward declarations (which is explicitely allowed)
274	# -Wchar-subscripts reports too many bogus warnings for "array['x']" (when 'x' is known to be in range [0..128])
275	# -Wunused-private-field report too many false positives (currently ~ 2 of 3)
276	# -Wstring-plus-int warns about common ARB coding practice
277	# -Wgnu-static-float-init warns about accepted GNU extension
278	extended_cpp_warnings += -Wno-mismatched-tags -Wno-char-subscripts -Wno-unused-private-field -Wno-string-plus-int -Wno-gnu-static-float-init
279	endif
280
281	#---------------------- developer
282
283	ifneq ($(DEVELOPER),ANY) # ANY=default setting (skip all developer specific code)
284	dflags += -DDEVEL_$(DEVELOPER)# activate developer/release specific code
285	endif
286
287	ifndef SHOWTODO
288	ifeq ($(DEVELOPER),RALF)
289	SHOWTODO:=1
290	else
291	SHOWTODO:=0
292	endif
293	endif
294	ifeq ($(SHOWTODO),1)
295	dflags += -DWARN_TODO# activate "TODO" warnings
296	endif
297
298	#---------------------- 32 or 64 bit
299
300	ifndef BUILDHOST_64
301	BUILDHOST_64:=$(ARB_64)# assume build host is same as version (see config.makefile)
302	endif
303
304	cross_cflags:=
305	cross_lflags:=
306	cross_clflags:=
307
308	ifeq ($(ARB_64),1)
309	dflags += -DARB_64 #-fPIC
310	shared_cflags += -fPIC
311
312	ifeq ($(BUILDHOST_64),1)
313	# build 64-bit ARB version on 64-bit host
314	CROSS_LIB:=# empty = autodetect below
315	ifeq ($(DARWIN),1)
316	cross_cflags += -arch x86_64
317	cross_lflags += -arch x86_64
318	cross_clflags += -arch x86_64
319	endif
320	else
321	# build 64-bit ARB version on 32-bit host
322	CROSS_LIB:=/lib64
323	cross_cflags += -m64
324	cross_lflags += -m64 -m elf_x86_64
325	cross_clflags += -m64 -Wl,-m64,-m,elf_x86_64
326	endif
327	else
328	ifeq ($(BUILDHOST_64),1)
329	# build 32-bit ARB version on 64-bit host
330	CROSS_LIB:=# empty = autodetect below
331	cross_cflags += -m32
332	cross_lflags += -m32 -m elf_i386
333	cross_clflags += -m32 -Wl,-m32,-m,elf_i386
334	else
335	# build 32-bit ARB version on 32-bit host
336	CROSS_LIB:=/lib
337	endif
338	endif
339
340	cflags += $(cross_cflags)
341	lflags += $(cross_lflags)
342	clflags += $(cross_clflags)
343
344	ifeq ('$(CROSS_LIB)','')
345	# autodetect libdir
346	ifeq ($(ARB_64),1)
347	CROSS_LIB:=$(shell (test -d /lib64 && echo lib64) \|\| echo lib)
348	else
349	CROSS_LIB:=$(shell (test -d /lib32 && echo lib32) \|\| echo lib)
350	endif
351	endif
352
353	#---------------------- unit tests
354
355	ifndef UNIT_TESTS
356	UNIT_TESTS=0#default is "no tests"
357	endif
358	ifeq ($(UNIT_TESTS),1)
359	dflags += -DUNIT_TESTS
360	UNIT_TESTER_LIB=UNIT_TESTER/UNIT_TESTER.a
361	else
362	UNIT_TESTER_LIB=
363	endif
364
365	#---------------------- use gcov
366
367	ifndef COVERAGE
368	COVERAGE=0#default is "no"
369	endif
370	ifneq ($(COVERAGE),0)
371	GCOVFLAGS=-ftest-coverage -fprofile-arcs
372	cflags += $(GCOVFLAGS)
373	EXECLIBS=-lgcov
374	else
375	GCOVFLAGS=
376	EXECLIBS=
377	endif
378
379	#---------------------- other flags
380
381	dflags += -D$(MACH) # define machine
382
383	ifeq ($(DARWIN),1)
384	shared_cflags += -fno-common
385	else
386	dflags += $(shell getconf LFS_CFLAGS)
387	endif
388
389	cflags += -pipe
390	cflags += -fmessage-length=0# don't wrap compiler output
391	cflags += -fshow-column# show columns
392	cflags += -funit-at-a-time
393	cflags += -fPIC
394	cflags += -fno-common# link all global data into one namespace
395	cflags += -fstrict-aliasing# gcc 3.4
396	ifeq ('$(USE_GCC_48_OR_HIGHER)','yes')
397	cflags += -fno-diagnostics-show-caret#gcc 4.8 (4.7.?)
398	endif
399	#cflags += -save-temps# uncomment to see preprocessor output
400
401	#---------------------- X11 location
402
403	ifeq ($(DARWIN),1)
404	XHOME:=$(PREFIX)
405	else
406	ifeq ($(DEBIAN),1)
407	XHOME:=$(PREFIX)
408	else
409	XHOME:=/usr/X11R6
410	endif
411	endif
412
413	XINCLUDES:=-I$(XHOME)/include
414	ifeq ($(DARWIN),1)
415	XINCLUDES += -I$(OSX_FW)/GLUT.framework/Headers -I$(OSX_FW)/OpenGL.framework/Headers -I$(OSX_SDK)/usr/include/krb5
416
417	XLIBS := -L$(XHOME)/lib -lXm -lpng -lz -lXt -lX11 -lXext -lXp -lXmu -lXi
418	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGL.dylib:$(OSX_FW_OPENGL)/libGL.dylib
419	XLIBS += -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGLU.dylib:$(OSX_FW_OPENGL)/libGLU.dylib
420	else
421	XLIBS:=-L$(XHOME)/$(CROSS_LIB) -lXm -lXpm -lXt -lXext -lX11
422	endif
423
424	#---------------------- open GL
425
426	ifeq ($(OPENGL),1)
427	cflags += -DARB_OPENGL # activate OPENGL code
428	GL := gl # this is the name of the OPENGL base target
429	GL_LIB_SYS := -lGL -lGLU
430	GL_LIB_ARB := -L$(ARBHOME)/GL/glAW -lglAW
431
432	ifeq ($(DARWIN),1)
433	GL_LIB_SYS += -lpthread
434	endif
435
436	GL_PNGLIBS_ARB := -L$(ARBHOME)/GL/glpng -lglpng_arb
437	GL_PNGLIBS_SYS := -lpng
438
439	GLEWLIB := -lGLEW -lGLw
440	ifeq ($(DARWIN),1)
441	GLUTLIB := -glut
442	else
443	GLUTLIB := -lglut
444	endif
445
446	GL_LIBS_SYS := $(GL_LIB_SYS) $(GL_PNGLIBS_SYS) $(GLEWLIB) $(GLUTLIB)
447	GL_LIBS_ARB := $(GL_LIB_ARB) $(GL_PNGLIBS_ARB)
448
449	RNA3D_LIB := RNA3D/RNA3D.a
450
451	else
452
453	GL_LIBS_ARB:=# no opengl -> no libs
454	GL_LIBS_SYS:=# no opengl -> no libs
455	GL:=# don't build ARB openGL libs
456
457	RNA3D_LIB :=
458
459	endif
460
461	RNA3D_LIB_4_DEPENDS := RNA3D/RNA3D.a
462
463	GL_LIBS:=$(GL_LIBS_ARB) $(GL_LIBS_SYS)
464
465	#---------------------- tiff lib:
466
467	TIFFLIBS := -ltiff
468
469	#---------------------- glib:
470
471	ARB_NEEDED_GLIB=glib-2.0
472
473	ARB_GLIB_INCLUDE:=$(strip $(shell pkg-config --cflags $(ARB_NEEDED_GLIB)))
474	ARB_GLIB_LIBS:=$(strip $(shell pkg-config --libs $(ARB_NEEDED_GLIB)))
475
476	#---------------------- basic libs:
477
478	SYSLIBS:=
479
480	ifeq ($(DARWIN),1)
481	SYSLIBS += -lstdc++
482	else
483	SYSLIBS += -lm $(ARB_GLIB_LIBS)
484	endif
485
486	#---------------------- include symbols?
487
488	ifeq ($(TRACESYM),1)
489	ifeq ($(USE_CLANG),0)
490	cflags += -rdynamic
491	lflags += --export-dynamic
492	clflags += -rdynamic -Wl,--export-dynamic
493	endif
494	endif
495
496	#---------------------- system dependent commands
497
498	ifeq ($(DARWIN),1)
499	TIME:=gtime
500	else
501	TIME:=/usr/bin/time
502	endif
503
504	# -------------------------------------------------------------------------
505	# Don't put any machine/version/etc conditionals below!
506	# (instead define variables above)
507	# -------------------------------------------------------------------------
508
509	cflags += -W -Wall $(dflags) $(extended_warnings)
510	cxxflags := $(extended_cpp_warnings)
511
512	# add CFLAGS + CPPFLAGS from environment for DEBIAN build
513	ifeq ($(DEBIAN),1)
514	cflags := $(CFLAGS) $(cflags)
515	cxxflags += $(CPPFLAGS)
516	endif
517
518	ifeq ('$(USE_GCC_47_OR_HIGHER)','yes')
519	cxxflags += -std=gnu++11# see also TEMPLATES/cxxforward.h@USE_Cxx11
520	else
521	# only use for gcc versions between 4.3 and <4.7 (4.7++ adds -Wc++11-compat above)
522	HAVE_GNUPP0X=`SOURCE_TOOLS/requireVersion.pl 4.3 $(COMPILER_VERSION)`
523	ifeq ($(HAVE_GNUPP0X),1)
524	# ensure compatibility with upcoming C++ standard
525	cxxflags += -std=gnu++0x
526	endif
527	endif
528
529	LINK_STATIC_LIB := ld $(lflags) -r -o# link static lib
530	LINK_EXECUTABLE := $(A_CXX) $(clflags) -o# link executable (c++)
531
532	ifeq ($(LINK_STATIC),1)
533	SHARED_LIB_SUFFIX = a# static lib suffix
534	LINK_SHARED_LIB := $(LINK_STATIC_LIB)
535	else
536	SHARED_LIB_SUFFIX = so# shared lib suffix
537	LINK_SHARED_LIB := $(A_CXX) $(clflags) -shared $(GCOVFLAGS) -o# link shared lib
538	endif
539
540	# delete variables unused below
541	lflags:=
542	clflags:=
543
544	# other used tools
545	MAKEDEPEND_PLAIN = makedepend
546	MAKEDEPEND = $(FORCEMASK);$(MAKEDEPEND_PLAIN)
547
548	#SEP:=--------------------------------------------------------------------------------
549	SEP=[`date +%M:%S.%N`] ------------------------------------------------
550	# to analyse timings run
551	# make -j9 clean; make -j9 all \| grep '^\[' \| sort
552	# make -j9 "TIMED_TARGET=perl" clean_timed_target \| grep '^\[' \| sort
553
554	CORE_LIB=-lCORE
555	ARBDB_LIB=-lARBDB $(CORE_LIB)
556	LIBS = $(ARBDB_LIB) $(SYSLIBS)
557
558	GUI_LIBS_PREFIX:=
559	ifeq ($(DARWIN),1)
560	# this seem to be added at wrong place, since opengl is only needed to link EDIT4
561	GUI_LIBS_PREFIX:=-framework GLUT -framework OpenGL
562	endif
563
564	GUI_LIBS=$(GUI_LIBS_PREFIX) $(LIBS) -lAWT -lWINDOW
565	GUI_LIBS+=$(XLIBS)
566
567	LIBPATH = -L$(ARBHOME)/lib
568
569	DEST_LIB = lib
570	DEST_BIN = bin
571
572	CC_INCLUDES := -I. -I$(ARBHOME)/INCLUDE $(XINCLUDES) $(ARB_GLIB_INCLUDE)
573	CXX_INCLUDES := $(CC_INCLUDES)
574	MAKEDEPENDFLAGS := -- -DARB_OPENGL -DUNIT_TESTS -D__cplusplus -I. -Y$(ARBHOME)/INCLUDE
575
576	# -------------------------------
577	# old PTSERVER or PTPAN?
578
579	ifeq ($(PTPAN),1)
580	# PTPAN only libs
581	ARCHS_PT_SERVER = \
582	ptpan/PROBE.a
583	else
584	ifeq ($(PTPAN),2)
585	# special mode to compile both servers (developers only!)
586	ARCHS_PT_SERVER = \
587	ptpan/PROBE.a \
588	PROBE/PROBE.a
589	ARCHS_PT_SERVER_LINK = PROBE/PROBE.a# default to old ptserver
590	else
591	# PT-server only libs
592	ARCHS_PT_SERVER = \
593	PROBE/PROBE.a
594	endif
595	endif
596
597	ifndef ARCHS_PT_SERVER_LINK
598	ARCHS_PT_SERVER_LINK = $(ARCHS_PT_SERVER)
599	endif
600
601	# ---------------------------------------
602	# wrap main()
603
604	use_ARB_main=$(ARBHOME)/SOURCE_TOOLS/arb_main_cpp.o
605	use_ARB_main_C=$(ARBHOME)/SOURCE_TOOLS/arb_main_c.o
606
607	# -----------------------------------------
608	# export variables to submakefiles
609
610	include SOURCE_TOOLS/export2sub
611
612	# do not define (exported) variables below this point
613
614	# -------------------------
615	# Main arb targets:
616	# -------------------------
617
618	first_target:
619	$(MAKE) checks
620	@echo $(SEP)
621	@echo 'Main targets:'
622	@echo ''
623	@echo ' all - Compile ARB + TOOLs + and copy shared libs + link foreign software'
624	@echo ' (That is most likely the target you want)'
625	@echo ''
626	@echo ' clean - remove generated files ("SUBDIR/SUBDIR.clean" to clean only SUBDIR)'
627	@echo ' rebuild - clean + all'
628	@echo ' relink - remove all binaries and relink them from objects'
629	@echo ''
630	@echo 'Some often used sub targets (make all makes them all):'
631	@echo ''
632	@echo ' arb - Just compile ARB (but none of the integrated tools)'
633	@echo ' menus - create lib/gde/arb.menu from GDEHELP/ARB_GDEmenus.source'
634	@echo ' perl - Compile the PERL XSUBS into lib/ARB.so and create links in lib to perl'
635	@echo ' binlink - Create all links in the bin directory'
636	@echo ''
637	@echo 'Development targets:'
638	@echo ''
639	@echo ' depends - create or update dependencies ("SUBDIR/SUBDIR.depends" to update only SUBDIR)'
640	@echo ' proto - create or update prototypes ("SUBDIR/SUBDIR.proto" to update only SUBDIR)'
641	@echo ' tags - create tags for xemacs'
642	@echo ' show - show available shortcuts (AKA subtargets)'
643	@echo ' up - shortcut for depends+proto+tags'
644	ifeq ($(UNIT_TESTS),1)
645	@echo ' ut - only run tests'
646	endif
647	@echo ' modified - rebuild files modified in svn checkout (does touch)'
648	@echo ' touch - touch files modified in svn checkout'
649	@echo ''
650	@echo 'Internal maintenance:'
651	@echo ''
652	@echo ' relinfo - show help on release targets'
653	@echo ' tarfile - make rebuild and create arb version tarfile ("tarfile_quick" to skip rebuild)'
654	@echo ' save - save all basic ARB sources into arbsrc_DATE ("savetest" to check filelist)'
655	@echo ' patch - save svn diff to patchfile'
656	@echo ' source_doc - create doxygen documentation'
657	@echo ' relocated - rebuild partly (use when you have relocated ARBHOME)'
658	@echo ' check_res - check ressource usage'
659	@echo ' dep_graph - Build dependency graphs'
660	@echo ' clean_cov - Clean coverage results'
661	@echo ''
662	@echo ' post_commit_check - Checks whether'
663	@echo ' * main make targets work,'
664	@echo ' * dependencies and prototypes are up to date,'
665	@echo ' * SVN-controlled files remain unaffected by called targets and'
666	@echo ' * all generated files are ignored.'
667	@echo ' (has to be called in a clean SVN checkout)'
668	@echo $(SEP)
669	@echo ''
670
671	relinfo:
672	@echo ''
673	@echo $(SEP)
674	@echo 'Release targets:'
675	@echo ''
676	@echo ' inc_candi - increase RC candidate-number (only possible in "rc" branch, not needed for RC1)'
677	@echo ' inc_patch - increase release patchlevel (only possible in "stable" branch)'
678	@echo ' inc_minor - increase minor version number (only possible in "trunk")'
679	@echo ' inc_major - increase MAJOR version number (only possible in "trunk")'
680	@echo ''
681	@echo ' show_version - show version tag'
682	@echo ''
683	@echo $(SEP)
684	@echo ''
685
686	# auto-generate config.makefile:
687
688	CONFIG_MAKEFILE_FOUND=$(wildcard config.makefile)
689
690	config.makefile : config.makefile.template
691	@echo --------------------------------------------------------------------------------
692	ifeq ($(strip $(CONFIG_MAKEFILE_FOUND)),)
693	@cp $< $@
694	@echo '$(ARBHOME)/$@:1: has been generated.'
695	@echo 'Please edit $@ to configure your system!'
696	@echo --------------------------------------------------------------------------------
697	@false
698	else
699	@echo '$(ARBHOME)/$<:1: is more recent than'
700	@echo '$(ARBHOME)/$@:1:'
701	@ls -al config.makefile*
702	@echo --------------------------------------------------------------------------------
703	@echo "Updating $@ (if this fails, check manually)"
704	SOURCE_TOOLS/update_config_makefile.pl
705	@echo "Sucessfully updated $@"
706	@echo --------------------------------------------------------------------------------
707	@ls -al config.makefile*
708	@echo --------------------------------------------------------------------------------
709	@echo "Diff to your old config.makefile:"
710	@echo --------------------------------------------------------------------------------
711	-diff $@.bak $@
712	@echo --------------------------------------------------------------------------------
713	endif
714
715	# check if everything is configured correctly
716
717	check_DEVELOPER:
718	ifndef DEVELOPER
719	@echo 'config.makefile:1: DEVELOPER not defined'
720	@false
721	endif
722
723	check_DEBUG:
724	ifndef dflags
725	@echo 'config.makefile:1: DEBUG has to be defined. Valid values are 0 and 1'
726	@false
727	endif
728
729	check_ARB_64:
730	ifndef ARB_64
731	@echo 'config.makefile:1: ARB_64 has to be defined. Valid values are 0 and 1'
732	@false
733	endif
734
735	# ---------------------------------------- check gcc version
736
737	check_same_GCC_VERSION:
738	$(ARBHOME)/SOURCE_TOOLS/check_same_compiler_version.pl $(COMPILER_NAME) $(COMPILER_VERSION_ALLOWED)
739
740	check_GCC_VERSION:
741	@echo 'Compiler version check:'
742	ifeq ('$(COMPILER_VERSION_ALLOWED)', '')
743	@echo " - Your compiler is '$(COMPILER_NAME)' version '$(COMPILER_VERSION)'"
744	@echo ' This version is not in the list of supported $(COMPILER_NAME)-versions:'
745	@$(foreach version,$(ALLOWED_COMPILER_VERSIONS),echo ' * $(version)';)
746	@echo ' - You may either ..'
747	@echo ' - add your version to ALLOWED_$(COMPILER_NAME)_VERSIONS in the Makefile and try it out or'
748	@echo ' - switch to one of the allowed versions (see arb_README_gcc.txt for installing'
749	@echo ' a different version of gcc)'
750	@echo ''
751	@false
752	else
753	@echo " - Supported $(COMPILER_NAME) version '$(COMPILER_VERSION_ALLOWED)' detected - fine!"
754	@echo ''
755	$(MAKE) check_same_GCC_VERSION
756
757	endif
758
759	#---------------------- check ARBHOME
760
761	# use arb_INSTALL.txt to determine whether ARBHOME points to correct directory
762	ARB_INSTALL_FOUND=$(wildcard $(ARBHOME)/arb_INSTALL.txt)
763
764	check_ARBHOME:
765	ifeq ($(strip $(ARB_INSTALL_FOUND)),)
766	@echo ------------------------------------------------------------
767	@echo "ARBHOME is set to '$(ARBHOME)'"
768	@echo "The environment variable ARBHOME has to point to the top arb source directory."
769	@echo "If you use bash enter:"
770	@echo " export ARBHOME='`pwd`'"
771	@echo ------------------------------------------------------------
772	@false
773	endif
774
775	ARB_PATH_SET=$(findstring $(ARBHOME)/bin,$(PATH))
776
777	check_PATH: check_ARBHOME
778	ifeq ($(strip $(ARB_PATH_SET)),)
779	@echo ------------------------------------------------------------
780	@echo "The environment variable PATH has to contain $(ARBHOME)/bin"
781	@echo "If you use bash enter:"
782	@echo ' export PATH=$$ARBHOME/bin:$$PATH'
783	@echo ------------------------------------------------------------
784	@false
785	endif
786
787	check_TOOLS:
788	@util/arb_check_build_env.pl \
789	"$(A_CC)" \
790	"$(A_CXX)" \
791	"$(MAKEDEPEND_PLAIN)" \
792	"$(LINK_SHARED_LIB)" \
793	"$(LINK_SHARED_LIB)" \
794
795
796	check_ENVIRONMENT : check_PATH check_TOOLS
797	@echo "-------------------- Environment [start]"
798	@echo "ARBHOME='$(ARBHOME)'"
799	@echo "PATH='$(PATH)'"
800	@echo "LD_LIBRARY_PATH='$(LD_LIBRARY_PATH)'"
801	@echo "-------------------- Environment [end]"
802
803	check_tabs: check_setup
804	ifeq ($(DEBUG),1)
805	@SOURCE_TOOLS/tabBrake.pl
806	endif
807
808	force_tab_check:
809	@touch -t 198001010000 SOURCE_TOOLS/stamp.tabBrake
810	@$(MAKE) check_tabs
811
812
813	# ---------------------
814
815	check_setup: check_ENVIRONMENT check_DEBUG check_ARB_64 check_DEVELOPER check_GCC_VERSION
816	@echo Your setup seems to be ok.
817
818	checks: check_setup check_tabs
819	@rm -f SOURCE_TOOLS/postcompile.sav
820
821
822	# end test section ------------------------------
823
824	# ---------------------------------------
825	# List of standard top level directories
826	#
827	# sub-makefiles have to define the targets
828	# - 'depends' and
829	# - 'clean'
830	#
831	# when adding new libs here, also add a dependency vs 'links' or 'links_non_perl' in .@DD_links_non_perl
832
833	ARCHS = \
834	$(ARCHS_PT_SERVER) \
835	AISC/AISC.a \
836	AISC_MKPTPS/AISC_MKPTPS.a \
837	ARBDB/libARBDB.a \
838	CORE/libCORE.a \
839	ARB_GDE/ARB_GDE.a \
840	AWT/libAWT.a \
841	AWTC/AWTC.a \
842	AWTI/AWTI.a \
843	CONSENSUS_TREE/CONSENSUS_TREE.a \
844	CONVERTALN/CONVERTALN.a \
845	DBSERVER/DBSERVER.a \
846	DIST/DIST.a \
847	EDIT4/EDIT4.a \
848	EISPACK/EISPACK.a \
849	GDE/GDE.a \
850	GENOM/GENOM.a \
851	GENOM_IMPORT/GENOM_IMPORT.a \
852	GL/GL.a \
853	ISLAND_HOPPING/ISLAND_HOPPING.a \
854	MERGE/MERGE.a \
855	MULTI_PROBE/MULTI_PROBE.a \
856	NALIGNER/NALIGNER.a \
857	NAMES/NAMES.a \
858	NAMES_COM/server.a \
859	NTREE/NTREE.a \
860	PARSIMONY/PARSIMONY.a \
861	PERLTOOLS/PERLTOOLS.a \
862	PHYLO/PHYLO.a \
863	PRIMER_DESIGN/PRIMER_DESIGN.a \
864	PROBE_COM/server.a \
865	PROBE_DESIGN/PROBE_DESIGN.a \
866	PROBE_SET/PROBE_SET.a \
867	READSEQ/READSEQ.a \
868	RNA3D/RNA3D.a \
869	RNACMA/RNACMA.a \
870	SECEDIT/SECEDIT.a \
871	SEQ_QUALITY/SEQ_QUALITY.a \
872	SERVERCNTRL/SERVERCNTRL.a \
873	SL/SL.a \
874	STAT/STAT.a \
875	TOOLS/TOOLS.a \
876	TREEGEN/TREEGEN.a \
877	UNIT_TESTER/UNIT_TESTER.a \
878	WETC/WETC.a \
879	WINDOW/libWINDOW.a \
880	XML/XML.a \
881
882	# -----------------------
883	# library packets
884
885	ARCHS_CLIENT_PROBE = PROBE_COM/client.a PROBE_COM/common.a
886	ARCHS_CLIENT_NAMES = NAMES_COM/client.a NAMES_COM/common.a
887
888	ARCHS_SERVER_PROBE = PROBE_COM/server.a $(ARCHS_CLIENT_PROBE)
889	ARCHS_SERVER_NAMES = NAMES_COM/server.a $(ARCHS_CLIENT_NAMES)
890
891	ARCHS_MAKEBIN = AISC_MKPTPS/AISC_MKPTPS.a AISC/AISC.a
892
893	# communication libs need aisc and aisc_mkpts:
894
895	AISC/AISC.dummy: proto_tools
896
897	comtools: AISC/AISC.dummy
898
899	ARCHS_SEQUENCE = \
900	SL/SEQUENCE/SEQUENCE.a \
901	SL/ALIVIEW/ALIVIEW.a \
902	SL/PRONUC/PRONUC.a \
903
904	ARCHS_TREE = \
905	$(ARCHS_SEQUENCE) \
906	SL/FILTER/FILTER.a \
907	SL/ARB_TREE/ARB_TREE.a \
908	SL/ROOTED_TREE/ROOTED_TREE.a \
909
910	# parsimony tree (used by NTREE, PARSIMONY, STAT(->EDIT4), DIST(obsolete!))
911	ARCHS_AP_TREE = \
912	$(ARCHS_TREE) \
913	SL/AP_TREE/AP_TREE.a \
914
915	# --------------------------------------------------------------------------------
916	# dependencies for linking shared libs
917
918	link_core: core
919	link_db: db link_core
920	link_aw: aw link_db
921	link_awt: awt link_aw
922
923	#***************************************************************************************
924	# Individual_Programs_Section
925	#***************************************************************************************
926
927	arbmainwrapper:
928	$(MAKE) -C SOURCE_TOOLS -r mainwrapper
929
930
931	#********************************* arb_ntree ************************************
932	NTREE = bin/arb_ntree
933	ARCHS_NTREE = \
934	NTREE/NTREE.a \
935	$(ARCHS_AP_TREE) \
936	ARB_GDE/ARB_GDE.a \
937	AWTC/AWTC.a \
938	AWTI/AWTI.a \
939	CONSENSUS_TREE/CONSENSUS_TREE.a \
940	GENOM/GENOM.a \
941	GENOM_IMPORT/GENOM_IMPORT.a \
942	MERGE/MERGE.a \
943	MULTI_PROBE/MULTI_PROBE.a \
944	PRIMER_DESIGN/PRIMER_DESIGN.a \
945	PROBE_DESIGN/PROBE_DESIGN.a \
946	SEQ_QUALITY/SEQ_QUALITY.a \
947	SERVERCNTRL/SERVERCNTRL.a \
948	SL/AW_NAME/AW_NAME.a \
949	SL/DB_UI/DB_UI.a \
950	SL/DB_SCANNER/DB_SCANNER.a \
951	SL/DB_QUERY/DB_QUERY.a \
952	SL/SEQIO/SEQIO.a \
953	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
954	SL/HELIX/HELIX.a \
955	SL/REGEXPR/REGEXPR.a \
956	SL/REFENTRIES/REFENTRIES.a \
957	SL/NDS/NDS.a \
958	SL/ITEMS/ITEMS.a \
959	SL/INSDEL/INSDEL.a \
960	SL/LOCATION/LOCATION.a \
961	SL/MACROS/MACROS.a \
962	SL/TRANSLATE/TRANSLATE.a \
963	SL/TREEDISP/TREEDISP.a \
964	SL/TREE_ADMIN/TREE_ADMIN.a \
965	SL/TREE_READ/TREE_READ.a \
966	SL/TREE_WRITE/TREE_WRITE.a \
967	STAT/STAT.a \
968	XML/XML.a \
969
970	$(NTREE): $(ARCHS_NTREE:.a=.dummy) link_awt
971	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NTREE) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
972	echo "$(SEP) Link $@"; \
973	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS)" ; \
974	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS) && \
975	echo "$(SEP) Link $@ [done]"; \
976	)
977
978	#********************************* arb_edit4 ************************************
979	EDIT4 = bin/arb_edit4
980
981	ARCHS_EDIT4 := \
982	EDIT4/EDIT4.a \
983	$(ARCHS_AP_TREE) \
984	ARB_GDE/ARB_GDE.a \
985	AWTC/AWTC.a \
986	ISLAND_HOPPING/ISLAND_HOPPING.a \
987	SECEDIT/SECEDIT.a \
988	SERVERCNTRL/SERVERCNTRL.a \
989	SL/AW_HELIX/AW_HELIX.a \
990	SL/AW_NAME/AW_NAME.a \
991	SL/FAST_ALIGNER/FAST_ALIGNER.a \
992	SL/ITEMS/ITEMS.a \
993	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
994	SL/HELIX/HELIX.a \
995	SL/TRANSLATE/TRANSLATE.a \
996	SL/MACROS/MACROS.a \
997	SL/NDS/NDS.a \
998	STAT/STAT.a \
999	XML/XML.a \
1000
1001	ifeq ($(OPENGL),1)
1002	ARCHS_EDIT4 += RNA3D/RNA3D.a
1003	endif
1004
1005	LIBS_EDIT4 := $(GL_LIBS)
1006
1007	$(EDIT4): $(ARCHS_EDIT4:.a=.dummy) link_awt
1008	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_EDIT4) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1009	echo "$(SEP) Link $@"; \
1010	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4) $(EXECLIBS)" ; \
1011	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_EDIT4) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(LIBS_EDIT4) $(EXECLIBS) && \
1012	echo "$(SEP) Link $@ [done]"; \
1013	)
1014
1015	#********************************* arb_rnacma ************************************
1016	RNACMA = bin/arb_rnacma
1017	ARCHS_RNACMA = \
1018	RNACMA/RNACMA.a \
1019
1020	$(RNACMA) : $(ARCHS_RNACMA:.a=.dummy) link_db
1021	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_RNACMA) \|\| ( \
1022	echo "$(SEP) Link $@"; \
1023	echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_RNACMA) $(LIBS) $(EXECLIBS)"; \
1024	$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_RNACMA) $(LIBS) $(EXECLIBS) && \
1025	echo "$(SEP) Link $@ [done]"; \
1026	)
1027
1028	#********************************* arb_wetc ************************************
1029	WETC = bin/arb_wetc
1030	ARCHS_WETC = \
1031	WETC/WETC.a \
1032	SL/HELIX/HELIX.a \
1033	SL/FILTER/FILTER.a \
1034	XML/XML.a \
1035
1036	$(WETC): $(ARCHS_WETC:.a=.dummy) link_awt
1037	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_WETC) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1038	echo "$(SEP) Link $@"; \
1039	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC) $(GUI_LIBS) $(EXECLIBS)" ; \
1040	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_WETC) $(GUI_LIBS) $(EXECLIBS) && \
1041	echo "$(SEP) Link $@ [done]"; \
1042	)
1043
1044	#********************************* arb_dist ************************************
1045	DIST = bin/arb_dist
1046	ARCHS_DIST = \
1047	$(ARCHS_AP_TREE) \
1048	CONSENSUS_TREE/CONSENSUS_TREE.a \
1049	DIST/DIST.a \
1050	EISPACK/EISPACK.a \
1051	SERVERCNTRL/SERVERCNTRL.a \
1052	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1053	SL/HELIX/HELIX.a \
1054	SL/MATRIX/MATRIX.a \
1055	SL/MACROS/MACROS.a \
1056	SL/NDS/NDS.a \
1057	SL/ITEMS/ITEMS.a \
1058	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.a \
1059	XML/XML.a \
1060
1061	$(DIST): $(ARCHS_DIST:.a=.dummy) link_awt
1062	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_DIST) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1063	echo "$(SEP) Link $@"; \
1064	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS)" ; \
1065	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DIST) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS) && \
1066	echo "$(SEP) Link $@ [done]"; \
1067	)
1068
1069	#********************************* arb_pars ************************************
1070	PARSIMONY = bin/arb_pars
1071	ARCHS_PARSIMONY = \
1072	$(ARCHS_AP_TREE) \
1073	PARSIMONY/PARSIMONY.a \
1074	SERVERCNTRL/SERVERCNTRL.a \
1075	SL/AW_NAME/AW_NAME.a \
1076	SL/GUI_ALIVIEW/GUI_ALIVIEW.a \
1077	SL/HELIX/HELIX.a \
1078	SL/MACROS/MACROS.a \
1079	SL/NDS/NDS.a \
1080	SL/ITEMS/ITEMS.a \
1081	SL/TRANSLATE/TRANSLATE.a \
1082	SL/TREEDISP/TREEDISP.a \
1083	XML/XML.a \
1084
1085	$(PARSIMONY): $(ARCHS_PARSIMONY:.a=.dummy) link_awt
1086	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PARSIMONY) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1087	echo "$(SEP) Link $@"; \
1088	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(EXECLIBS)" ; \
1089	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PARSIMONY) $(ARCHS_CLIENT_NAMES) $(GUI_LIBS) $(EXECLIBS) && \
1090	echo "$(SEP) Link $@ [done]"; \
1091	)
1092
1093	#********************************* arb_convert_aln ************************************
1094	CONVERT_ALN = bin/arb_convert_aln
1095	ARCHS_CONVERT_ALN = \
1096	CONVERTALN/CONVERTALN.a \
1097
1098	$(CONVERT_ALN) : $(ARCHS_CONVERT_ALN:.a=.dummy) link_db
1099	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_CONVERT_ALN) $(use_ARB_main) \|\| ( \
1100	echo "$(SEP) Link $@"; \
1101	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN) $(LIBS) $(EXECLIBS)"; \
1102	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_CONVERT_ALN) $(LIBS) $(EXECLIBS) && \
1103	echo "$(SEP) Link $@ [done]"; \
1104	)
1105
1106	#********************************* arb_treegen ************************************
1107
1108	TREEGEN = bin/arb_treegen
1109	ARCHS_TREEGEN = \
1110	TREEGEN/TREEGEN.a \
1111
1112	$(TREEGEN) : $(ARCHS_TREEGEN:.a=.dummy)
1113	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_TREEGEN) $(use_ARB_main_C) \|\| ( \
1114	echo "$(SEP) Link $@"; \
1115	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN) $(EXECLIBS)" ; \
1116	$(LINK_EXECUTABLE) $@ $(use_ARB_main_C) $(LIBPATH) $(ARCHS_TREEGEN) $(EXECLIBS) && \
1117	echo "$(SEP) Link $@ [done]"; \
1118	)
1119
1120	#********************************* arb_naligner ************************************
1121	NALIGNER = bin/arb_naligner
1122	ARCHS_NALIGNER = \
1123	NALIGNER/NALIGNER.a \
1124	SERVERCNTRL/SERVERCNTRL.a \
1125	SL/HELIX/HELIX.a \
1126
1127	$(NALIGNER): $(ARCHS_NALIGNER:.a=.dummy) link_db
1128	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NALIGNER) $(use_ARB_main) \|\| ( \
1129	echo "$(SEP) Link $@"; \
1130	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(LIBS) $(EXECLIBS)" ; \
1131	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NALIGNER) $(ARCHS_CLIENT_PROBE) $(LIBS) $(EXECLIBS) && \
1132	echo "$(SEP) Link $@ [done]"; \
1133	)
1134
1135	#********************************* arb_phylo ************************************
1136	PHYLO = bin/arb_phylo
1137	ARCHS_PHYLO = \
1138	PHYLO/PHYLO.a \
1139	SL/HELIX/HELIX.a \
1140	SL/FILTER/FILTER.a \
1141	SL/MATRIX/MATRIX.a \
1142	SL/MACROS/MACROS.a \
1143	XML/XML.a \
1144
1145	$(PHYLO): $(ARCHS_PHYLO:.a=.dummy) link_awt
1146	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PHYLO) $(GUI_LIBS) $(use_ARB_main) \|\| ( \
1147	echo "$(SEP) Link $@"; \
1148	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO) $(GUI_LIBS) $(EXECLIBS)" ; \
1149	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PHYLO) $(GUI_LIBS) $(EXECLIBS) && \
1150	echo "$(SEP) Link $@ [done]"; \
1151	)
1152
1153	#***************************************************************************************
1154	# SERVER SECTION
1155	#***************************************************************************************
1156
1157	#********************************* arb_db_server ************************************
1158	DBSERVER = bin/arb_db_server
1159	ARCHS_DBSERVER = \
1160	DBSERVER/DBSERVER.a \
1161	SERVERCNTRL/SERVERCNTRL.a \
1162
1163	$(DBSERVER): $(ARCHS_DBSERVER:.a=.dummy) link_db
1164	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_DBSERVER) $(ARBDB_LIB) $(use_ARB_main) \|\| ( \
1165	echo "$(SEP) Link $@"; \
1166	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS) $(EXECLIBS)" ; \
1167	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_DBSERVER) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) $(SYSLIBS) $(EXECLIBS) && \
1168	echo "$(SEP) Link $@ [done]"; \
1169	)
1170
1171	#********************************* arb_pt_server ************************************
1172	PROBE = bin/arb_pt_server
1173	ARCHS_PROBE_COMMON = \
1174	SERVERCNTRL/SERVERCNTRL.a \
1175	SL/HELIX/HELIX.a \
1176	SL/PTCLEAN/PTCLEAN.a \
1177
1178	ARCHS_PROBE_LINK = \
1179	$(ARCHS_PROBE_COMMON) \
1180	$(ARCHS_PT_SERVER_LINK) \
1181
1182	ARCHS_PROBE_DEPEND = \
1183	$(ARCHS_PROBE_COMMON) \
1184	$(ARCHS_PT_SERVER) \
1185
1186	$(PROBE): $(ARCHS_PROBE_DEPEND:.a=.dummy) link_db
1187	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_PROBE_LINK) $(ARBDB_LIB) $(ARCHS_CLIENT_PROBE) config.makefile $(use_ARB_main) \|\| ( \
1188	echo "$(SEP) Link $@"; \
1189	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_LINK) $(ARBDB_LIB) $(ARCHS_SERVER_PROBE) $(SYSLIBS) $(EXECLIBS)" ; \
1190	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_PROBE_LINK) $(ARBDB_LIB) $(ARCHS_SERVER_PROBE) $(SYSLIBS) $(EXECLIBS) && \
1191	echo "$(SEP) Link $@ [done]"; \
1192	)
1193
1194	#********************************* arb_name_server ************************************
1195	NAMES = bin/arb_name_server
1196	ARCHS_NAMES = \
1197	NAMES/NAMES.a \
1198	SERVERCNTRL/SERVERCNTRL.a \
1199
1200	$(NAMES): $(ARCHS_NAMES:.a=.dummy) link_db
1201	@SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) $(use_ARB_main) \|\| ( \
1202	echo "$(SEP) Link $@"; \
1203	echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS) $(EXECLIBS)" ; \
1204	$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NAMES) $(ARBDB_LIB) $(ARCHS_CLIENT_NAMES) NAMES_COM/server.a $(SYSLIBS) $(EXECLIBS) && \
1205	echo "$(SEP) Link $@ [done]"; \
1206	)
1207
1208	#********************************* SHARED LIBRARIES SECTION ************************************
1209
1210	prepare_libdir: addlibs
1211
1212	addlibs:
1213	(perl $(ARBHOME)/SOURCE_TOOLS/provide_libs.pl \
1214	"arbhome=$(ARBHOME)" \
1215	"opengl=$(OPENGL)" \
1216	"link_static=$(LINK_STATIC)" \
1217	)
1218
1219	#***************************************************************************************
1220	# Recursive calls to sub-makefiles
1221	#***************************************************************************************
1222
1223	%.depends:
1224	@cp -p $(@D)/Makefile $(@D)/Makefile.old # save old Makefile
1225	@$(MAKE) -C $(@D) -r \
1226	"AUTODEPENDS=1" \
1227	"MAIN=nothing" \
1228	"cflags=noCflagsHere_use_MAKEDEPENDFLAGS" \
1229	"cxxflags=noCxxflagsHere_use_MAKEDEPENDFLAGS" \
1230	depends
1231	@grep "^# DO NOT DELETE" $(@D)/Makefile >/dev/null
1232	@cat $(@D)/Makefile \
1233	\| SOURCE_TOOLS/fix_depends.pl "(from main)" \
1234	>$(@D)/Makefile.2
1235	@mv $(@D)/Makefile.old $(@D)/Makefile # restore old Makefile
1236	@$(ARBHOME)/SOURCE_TOOLS/mv_if_diff $(@D)/Makefile.2 $(@D)/Makefile # update Makefile if changed
1237
1238	%.proto:
1239	@$(MAKE) -C $(@D) \
1240	"AUTODEPENDS=0" \
1241	"MAIN=nothing" \
1242	"cflags=noCflags" \
1243	"cxxflags=noCxxflags" \
1244	proto
1245
1246	%.clean:
1247	@$(MAKE) -C $(@D) \
1248	"AUTODEPENDS=0" \
1249	"MAIN=nothing" \
1250	"cflags=noCflags" \
1251	"cxxflags=noCxxflags" \
1252	clean
1253
1254
1255	# stop wrong targets
1256	target_is_missing_lib_prefix:
1257	@echo "Error: Denied to build shared library target with missing 'lib'-prefix"
1258	false
1259
1260	ARBDB/ARBDB.dummy: target_is_missing_lib_prefix
1261	CORE/CORE.dummy: target_is_missing_lib_prefix
1262	AWT/AWT.dummy: target_is_missing_lib_prefix
1263	WINDOW/WINDOW.dummy: target_is_missing_lib_prefix
1264
1265	# rule to generate main target (normally a library):
1266	# @@@ check effect of setting LANG=C below
1267	%.dummy:
1268	@( export ID=$$$$; LANG=C; \
1269	(( \
1270	echo "$(SEP) Make $(@D)"; \
1271	$(MAKE) -C $(@D) -r \
1272	"AUTODEPENDS=1" \
1273	"MAIN=$(@F:.dummy=.a)" \
1274	"cflags=$(cflags) -DIN_ARB_$(subst /,_,$(@D))" \
1275	&& \
1276	echo "$(SEP) Make $(@D) [done]"; \
1277	) >$(@D).$$ID.log 2>&1 && (cat $(@D).$$ID.log;rm $(@D).$$ID.log)) \|\| (cat $(@D).$$ID.log;rm $(@D).$$ID.log;false))
1278
1279	# Additional dependencies for subtargets:
1280
1281	PROBE_COM/PROBE_COM.dummy : comtools
1282	NAMES_COM/NAMES_COM.dummy : comtools
1283
1284	com: PROBE_COM/PROBE_COM.dummy NAMES_COM/NAMES_COM.dummy
1285
1286	PROBE_COM/server.dummy:
1287	@echo Unwanted request to make target $<
1288	false
1289
1290	PROBE_COM/client.dummy:
1291	@echo Unwanted request to make target $<
1292	false
1293
1294	NAMES_COM/server.dummy:
1295	@echo Unwanted request to make target $<
1296	false
1297
1298	NAMES_COM/client.dummy:
1299	@echo Unwanted request to make target $<
1300	false
1301
1302
1303	ARBDB/libARBDB.dummy: links
1304	CORE/libCORE.dummy: links
1305
1306	PERLTOOLS/PERLTOOLS.dummy: core db
1307
1308	# all subdirs perl not depends on go here (ADD_links_non_perl)
1309	AWT/libAWT.dummy: links_non_perl
1310	AWTI/AWTI.dummy: links_non_perl
1311	CONSENSUS_TREE/CONSENSUS_TREE.dummy: links_non_perl
1312	CONVERTALN/CONVERTALN.dummy: links_non_perl
1313	DBSERVER/DBSERVER.dummy: links_non_perl
1314	DIST/DIST.dummy: links_non_perl
1315	EDIT4/EDIT4.dummy: links_non_perl genheaders com
1316	EISPACK/EISPACK.dummy: links_non_perl
1317	GDE/GDE.dummy: links_non_perl
1318	GENOM/GENOM.dummy: links_non_perl
1319	GENOM_IMPORT/GENOM_IMPORT.dummy: links_non_perl
1320	ISLAND_HOPPING/ISLAND_HOPPING.dummy: links_non_perl
1321	MERGE/MERGE.dummy: links_non_perl
1322	NTREE/NTREE.dummy: links_non_perl genheaders
1323	PARSIMONY/PARSIMONY.dummy: links_non_perl
1324	PHYLO/PHYLO.dummy: links_non_perl
1325	PRIMER_DESIGN/PRIMER_DESIGN.dummy: links_non_perl
1326	PROBE_SET/PROBE_SET.dummy: links_non_perl link_db
1327	READSEQ/READSEQ.dummy: links_non_perl
1328	RNACMA/RNACMA.dummy: links_non_perl header_libs
1329	SECEDIT/SECEDIT.dummy: links_non_perl
1330	SEQ_QUALITY/SEQ_QUALITY.dummy: links_non_perl
1331	SERVERCNTRL/SERVERCNTRL.dummy: links_non_perl com
1332	SL/ALIVIEW/ALIVIEW.dummy: links_non_perl
1333	SL/AP_TREE/AP_TREE.dummy: links_non_perl
1334	SL/ARB_TREE/ARB_TREE.dummy: links_non_perl
1335	SL/AW_HELIX/AW_HELIX.dummy: links_non_perl
1336	SL/DB_QUERY/DB_QUERY.dummy: links_non_perl
1337	SL/DB_SCANNER/DB_SCANNER.dummy: links_non_perl
1338	SL/DB_UI/DB_UI.dummy: links_non_perl
1339	SL/FAST_ALIGNER/FAST_ALIGNER.dummy: links_non_perl
1340	SL/FILTER/FILTER.dummy: links_non_perl
1341	SL/GUI_ALIVIEW/GUI_ALIVIEW.dummy: links_non_perl
1342	SL/HELIX/HELIX.dummy: links_non_perl
1343	SL/INSDEL/INSDEL.dummy: links_non_perl
1344	SL/ITEMS/ITEMS.dummy: links_non_perl
1345	SL/LOCATION/LOCATION.dummy: links_non_perl
1346	SL/MACROS/MACROS.dummy: links_non_perl
1347	SL/MATRIX/MATRIX.dummy: links_non_perl
1348	SL/NDS/NDS.dummy: links_non_perl
1349	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.dummy: links_non_perl
1350	SL/PRONUC/PRONUC.dummy: links_non_perl
1351	SL/PTCLEAN/PTCLEAN.dummy: links_non_perl link_db
1352	SL/REFENTRIES/REFENTRIES.dummy: links_non_perl
1353	SL/REGEXPR/REGEXPR.dummy: links_non_perl
1354	SL/ROOTED_TREE/ROOTED_TREE.dummy: links_non_perl
1355	SL/SEQIO/SEQIO.dummy: links_non_perl
1356	SL/SEQUENCE/SEQUENCE.dummy: links_non_perl
1357	SL/TRANSLATE/TRANSLATE.dummy: links_non_perl
1358	SL/TREE_ADMIN/TREE_ADMIN.dummy: links_non_perl
1359	SL/TREE_READ/TREE_READ.dummy: links_non_perl
1360	SL/TREE_WRITE/TREE_WRITE.dummy: links_non_perl
1361	SL/TREEDISP/TREEDISP.dummy: links_non_perl
1362	STAT/STAT.dummy: links_non_perl
1363	TREEGEN/TREEGEN.dummy: links_non_perl
1364	WETC/WETC.dummy: links_non_perl
1365	WINDOW/libWINDOW.dummy: links_non_perl
1366	XML/XML.dummy: links_non_perl
1367
1368	ifeq ($(OPENGL),1)
1369	GL/glAW/glAW.dummy: links_non_perl
1370	GL/glpng/glpng.dummy: links_non_perl
1371	GL/GL.dummy: GL/glAW/glAW.dummy GL/glpng/glpng.dummy
1372	RNA3D/RNA3D.dummy: links_non_perl gl
1373	endif
1374
1375	UNIT_TESTER/UNIT_TESTER.dummy: link_db \
1376	SERVERCNTRL/SERVERCNTRL.dummy \
1377
1378	TOOLS/TOOLS.dummy : links_non_perl link_db \
1379	SERVERCNTRL/SERVERCNTRL.dummy \
1380	SL/ROOTED_TREE/ROOTED_TREE.dummy \
1381	SL/TREE_WRITE/TREE_WRITE.dummy \
1382	SL/TREE_READ/TREE_READ.dummy \
1383	CONSENSUS_TREE/CONSENSUS_TREE.dummy \
1384	XML/XML.dummy \
1385
1386	AWTC/AWTC.dummy : com
1387
1388	NAMES/NAMES.dummy : com
1389	SL/AW_NAME/AW_NAME.dummy : com
1390
1391	PROBE/PROBE.dummy : com
1392	ptpan/PROBE.dummy : com
1393	MULTI_PROBE/MULTI_PROBE.dummy : com
1394	PROBE_DESIGN/PROBE_DESIGN.dummy : com
1395	NALIGNER/NALIGNER.dummy : com
1396
1397	ARB_GDE/ARB_GDE.dummy : proto_tools
1398
1399	compile_compatibility: SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.dummy
1400
1401	#***************************************************************************************
1402	# Short aliases to make targets
1403	#***************************************************************************************
1404
1405	show:
1406	@echo $(SEP)
1407	@echo 'Aliases for often needed targets:'
1408	@echo ''
1409	@echo ' executables:'
1410	@echo ''
1411	@echo ' nt arb_ntree'
1412	@echo ' e4 arb_edit4 (includes secedit)'
1413	@echo ' di arb_dist'
1414	@echo ' ph arb_phylo'
1415	@echo ' pa arb_parsimony'
1416	@echo ' tg arb_treegen'
1417	@echo ' ds arb_dbserver'
1418	@echo ' pt arb_pt_server'
1419	@echo ' na arb_name_server'
1420	@echo ''
1421	@echo ' libraries:'
1422	@echo ''
1423	@echo ' com communication libraries'
1424	@echo ' db ARB database'
1425	@echo ' aw GUI lib'
1426	@echo ' awt GUI toolkit'
1427	@echo ' awtc general purpose library'
1428	@echo ' awti import/export library'
1429	@echo ' mp multi probe library'
1430	@echo ' ge genome library'
1431	@echo ' pd probe design lib'
1432	@echo ' prd primer design lib'
1433	@echo ''
1434	@echo ' other targets:'
1435	@echo ''
1436	@echo ' help recompile help files'
1437	@echo ' tools make small tools used by arb'
1438	@echo ''
1439	@echo ' foreign targets:'
1440	@echo ''
1441	@echo ' gde GDE'
1442	@echo ' agde ARB_GDE'
1443	@echo ''
1444	@echo 'for other targets inspect $(ARBHOME)/Makefile'
1445	@echo ''
1446	@echo $(SEP)
1447
1448	source_doc:
1449	@echo "Remove some links (doxygen crashes otherwise):"
1450	find . \( -name "AISC" -o -name "C" -o -name "GDEHELP" \) -type l -exec rm {} \;
1451	doxygen 2>&1 1>/dev/null
1452	$(MAKE) forcelinks
1453
1454	dep_graph:
1455	@echo "Building some dependency graphs"
1456	SOURCE_TOOLS/dependency_graphs.pl
1457
1458	help: HELP_SOURCE/HELP_SOURCE.dummy
1459
1460	HELP_SOURCE/HELP_SOURCE.dummy: link_core xml menus
1461
1462	db: ARBDB/libARBDB.dummy
1463	core: CORE/libCORE.dummy
1464	aw: WINDOW/libWINDOW.dummy
1465	awt: AWT/libAWT.dummy
1466	awtc: AWTC/AWTC.dummy
1467	awti: AWTI/AWTI.dummy
1468
1469	mp: MULTI_PROBE/MULTI_PROBE.dummy
1470	mg: MERGE/MERGE.dummy
1471	ge: GENOM/GENOM.dummy
1472	prd: PRIMER_DESIGN/PRIMER_DESIGN.dummy
1473
1474	nt: menus $(NTREE)
1475
1476	nal: $(NALIGNER)
1477
1478	di: $(DIST)
1479	ph: $(PHYLO)
1480	pa: $(PARSIMONY)
1481	tg: $(TREEGEN)
1482
1483	ifeq ($(OPENGL),1)
1484	3d: RNA3D/RNA3D.dummy
1485	gl: GL/GL.dummy
1486	else
1487	noopengl:
1488	@echo "invalid target for OPENGL=0"
1489	3d: noopengl
1490	gl: noopengl
1491	endif
1492
1493	SL/SL.dummy: com
1494
1495	ds: $(DBSERVER)
1496	pt: $(PROBE)
1497	pst: PROBE_SET/PROBE_SET.dummy
1498	pd: PROBE_DESIGN/PROBE_DESIGN.dummy
1499	na: $(NAMES)
1500	sq: SEQ_QUALITY/SEQ_QUALITY.dummy
1501	cma: $(RNACMA)
1502
1503	sec: SECEDIT/SECEDIT.dummy
1504
1505	e4: $(EDIT4) readseq menus
1506
1507	gi: GENOM_IMPORT/GENOM_IMPORT.dummy
1508	wetc: $(WETC)
1509
1510	xml: XML/XML.dummy
1511	xmlin: XML_IMPORT/XML_IMPORT.dummy# broken
1512	stat: STAT/STAT.dummy $(NTREE) $(EDIT4)
1513	fa: SL/FAST_ALIGNER/FAST_ALIGNER.dummy
1514
1515	#********************************************************************************
1516
1517	up_by_remake: depends proto
1518
1519	up: up_by_remake tags valgrind_update
1520
1521	#********************************************************************************
1522
1523	touch:
1524	SOURCE_TOOLS/touch_modified.pl
1525
1526	modified: touch
1527	$(MAKE) all
1528
1529	#********************************************************************************
1530
1531	libdepends:
1532	$(MAKE) -C "SOURCE_TOOLS" \
1533	"RNA3D_LIB=$(RNA3D_LIB_4_DEPENDS)" \
1534	libdepends
1535
1536	#********************************************************************************
1537
1538	# create generated headers:
1539	genheaders: TEMPLATES/TEMPLATES.dummy
1540
1541	clrdotdepends:
1542	-rm PROBE_COM/.depends
1543	-rm NAMES_COM/.depends
1544	-rm PERL2ARB/.depends
1545
1546	comdepends: comtools clrdotdepends
1547	@echo "$(SEP) Partially build com interface"
1548	$(MAKE) PROBE_COM/PROBE_COM.depends NAMES_COM/NAMES_COM.depends
1549	$(MAKE) PROBE_COM/server.depends NAMES_COM/server.depends
1550
1551	depends: genheaders comdepends
1552	@echo "$(SEP) Updating other dependencies"
1553	$(MAKE) $(subst NAMES_COM/server.depends,,$(subst PROBE_COM/server.depends,,$(ARCHS:.a=.depends))) \
1554	HELP_SOURCE/HELP_SOURCE.depends \
1555	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.depends \
1556
1557	$(MAKE) libdepends
1558
1559	depend: depends
1560
1561	# ------------------------------------------------------------
1562	# dependency generation tests for AISC code
1563	#(all should work w/o creating wrong dependencies;
1564	# neither in XXX_COM/Makefile nor in code using AISC interface)
1565	dependstest1: silent_clean
1566	$(MAKE) depends
1567	dependstest2: silent_clean
1568	$(MAKE) com
1569	dependstest3: silent_clean
1570	$(MAKE) aw
1571	dependstest4: silent_clean
1572	$(MAKE) pt
1573	dependstest5: silent_clean
1574	$(MAKE) na
1575	dependstest6: silent_clean
1576	$(MAKE) nt
1577	dependstest7: silent_clean
1578	$(MAKE) all
1579	# ------------------------------------------------------------
1580
1581	AISC_MKPTPS/AISC_MKPTPS.dummy: links
1582
1583	proto_tools: AISC_MKPTPS/AISC_MKPTPS.dummy
1584
1585	proto: proto_tools
1586	@echo $(SEP) Updating prototypes
1587	$(MAKE) \
1588	ARBDB/ARBDB.proto \
1589	AISC_COM/AISC_COM.proto \
1590	ARB_GDE/ARB_GDE.proto \
1591	CORE/CORE.proto \
1592	CONVERTALN/CONVERTALN.proto \
1593	NTREE/NTREE.proto \
1594	MERGE/MERGE.proto \
1595	$(ARCHS_PT_SERVER:.a=.proto) \
1596	SERVERCNTRL/SERVERCNTRL.proto \
1597	SL/SL.proto \
1598
1599	#********************************************************************************
1600
1601	valgrind_update: links
1602	@echo $(SEP) Updating for valgrind
1603	$(MAKE) -C SOURCE_TOOLS valgrind_update
1604
1605	#********************************************************************************
1606
1607	TAGFILE=TAGS
1608	TAGFILE_TMP=TAGS.tmp
1609
1610	TAG_SOURCE_HEADERS=TAGS.headers
1611	TAG_SOURCE_CODE=TAGS.codefiles
1612	TAG_SOURCE_LISTS=$(TAG_SOURCE_HEADERS) $(TAG_SOURCE_CODE)
1613
1614	ETAGS=ctags -e -f $(TAGFILE_TMP) --sort=no --if0=no --extra=q
1615	ETAGS_TYPES=--C-kinds=cgnsut --C++-kinds=cgnsut
1616	ETAGS_FUN =--C-kinds=fm --C++-kinds=fm
1617	ETAGS_REST =--C-kinds=dev --C++-kinds=dev
1618
1619	FILTER_TAGS_SOURCES= \
1620	$(SED) -e 's/^.\///g' \| \
1621	grep -P -v -i '^HEADERLIBS\|^GDE/\|/GEN[CH]/'
1622
1623	$(TAG_SOURCE_HEADERS): links
1624	find . \( -name '.hxx' -o -name ".h" \) -type f \| $(FILTER_TAGS_SOURCES) > $@
1625
1626	$(TAG_SOURCE_CODE): links
1627	find . \( -name '.cxx' -o -name ".c" \) -type f \| $(FILTER_TAGS_SOURCES) > $@
1628
1629	tags: $(TAG_SOURCE_LISTS)
1630	$(ETAGS) $(ETAGS_TYPES) -L $(TAG_SOURCE_HEADERS)
1631	$(ETAGS) -a $(ETAGS_FUN) -L $(TAG_SOURCE_HEADERS)
1632	$(ETAGS) -a $(ETAGS_REST) -L $(TAG_SOURCE_HEADERS)
1633	$(ETAGS) -a $(ETAGS_TYPES) -L $(TAG_SOURCE_CODE)
1634	$(ETAGS) -a $(ETAGS_FUN) -L $(TAG_SOURCE_CODE)
1635	$(ETAGS) -a $(ETAGS_REST) -L $(TAG_SOURCE_CODE)
1636	mv_if_diff $(TAGFILE_TMP) $(TAGFILE)
1637	rm $(TAG_SOURCE_LISTS)
1638
1639	#********************************************************************************
1640
1641	LINKSTAMP=SOURCE_TOOLS/stamp.generate_all_links
1642
1643	links: checks $(LINKSTAMP) arbmainwrapper
1644	links_no_checks: $(LINKSTAMP) arbmainwrapper
1645
1646	forcelinks:
1647	-rm $(LINKSTAMP)
1648	$(MAKE) links
1649
1650	$(LINKSTAMP): SOURCE_TOOLS/generate_all_links.sh
1651	+SOURCE_TOOLS/generate_all_links.sh
1652	touch $(LINKSTAMP)
1653
1654	clean_links:
1655	# avoid to delete linked pts, nas or arb_tcp.dat:
1656	find . -path './lib' -prune -o -type l -exec rm {} \;
1657	# removed obsolete file - refuses to disappear due to 'prune' above
1658	@rm -f lib/help/GDEHELP
1659	@rm -f $(LINKSTAMP) lib/inputMasks/format.readme
1660
1661	redo_links: clean_links
1662	$(MAKE) links_no_checks
1663
1664	#********************************************************************************
1665
1666	header_libs:
1667	$(MAKE) -C HEADERLIBS all
1668
1669	#********************************************************************************
1670
1671	gde: GDE/GDE.dummy
1672	GDE: gde
1673	agde: ARB_GDE/ARB_GDE.dummy
1674
1675	tools: TOOLS/TOOLS.dummy
1676
1677	convert: $(CONVERT_ALN)
1678	readseq: READSEQ/READSEQ.dummy
1679
1680	#***************************************************************************************
1681	# Some user commands
1682	#***************************************************************************************
1683
1684	menus: binlink links
1685	@(( \
1686	echo "$(SEP) Make GDEHELP"; \
1687	$(MAKE) -C GDEHELP -r all && \
1688	echo "$(SEP) Make GDEHELP [done]"; \
1689	) > GDEHELP.log 2>&1 && (cat GDEHELP.log;rm GDEHELP.log)) \|\| (cat GDEHELP.log;rm GDEHELP.log;false)
1690
1691	ifeq ($(DEBUG),1)
1692	BIN_TARGET=develall
1693	else
1694	BIN_TARGET=all
1695	endif
1696
1697
1698	binlink:
1699	$(MAKE) -C bin $(BIN_TARGET)
1700
1701	preplib:
1702	(cd lib;$(MAKE) all)
1703
1704	# --------------------------------------------------------------------------------
1705	# This section is quite tricky:
1706	#
1707	# make 'perl' is a BIG target, so when it has to be made, it has to be started
1708	# as early as possible to reduce overall compile time. Since 'make' does not
1709	# provide any priotities, i force it to build all 'perl'-prerequisites early, by
1710	# adding artificial dependencies to these prerequisites
1711	#
1712	# That behavior is likely to be system-dependent.
1713	# My goal was only to make it work on my current development system,
1714	# where this saves about 20% of overall build time.
1715
1716	ifeq ($(WITHPERL),1)
1717	links_non_perl: PERLTOOLS/PERLTOOLS.dummy
1718	perltools: links_non_perl
1719	perl: realperl
1720	else
1721	links_non_perl: links
1722	perl:
1723	$(MAKE) "WITHPERL=1" perl
1724	endif
1725
1726	# ---------------------------------------- perl
1727
1728	ifeq ($(ARB_64),$(BUILDHOST_64))
1729	TEST_PERL_SCRIPTS=$(MAKE) -C PERL_SCRIPTS/test test
1730	else
1731	TEST_PERL_SCRIPTS=echo "skipping perl script compilation (when cross-compiling)"
1732	endif
1733
1734	realperl: perltools
1735	(( \
1736	echo "$(SEP) Make PERL2ARB" ; \
1737	$(TIME) $(MAKE) -C PERL2ARB -r -f Makefile.main \
1738	"AUTODEPENDS=1" \
1739	"dflags=$(dflags)" \
1740	"cross_cflags=$(cross_cflags) $(cxxflags) $(dflags)" \
1741	"cross_lflags=$(cross_lflags)" \
1742	"COMPILER_VERSION=$(COMPILER_VERSION)" \
1743	all && \
1744	$(TEST_PERL_SCRIPTS) && \
1745	echo "$(SEP) Make PERL2ARB [done]" ; \
1746	) > PERL2ARB.log 2>&1 && (cat PERL2ARB.log;rm PERL2ARB.log)) \|\| (cat PERL2ARB.log;rm PERL2ARB.log;false)
1747
1748	perl_clean:
1749	@$(MAKE) -C PERL2ARB -r -f Makefile.main \
1750	"AUTODEPENDS=0" \
1751	clean
1752
1753	PERL2ARB/PERL2ARB.clean:
1754	$(MAKE) perl_clean
1755	$(MAKE) -C PERL_SCRIPTS/test clean
1756
1757	# ---------------------------------------- bindings to script languages
1758
1759	bindings: lib/libCORE.so lib/libARBDB.so
1760	$(MAKE) -C BINDINGS all ARBDEPENDS="$(^:%=../%)" DFLAGS="$(dflags)"
1761
1762	bindings_clean:
1763	$(MAKE) -C BINDINGS clean
1764
1765	# ----------------------------------------
1766
1767	CLOC=cloc-1.08.pl
1768	CLOCFLAGS=--no3 --quiet --progress-rate=0
1769	CLOCARB=--exclude-dir=GDE .
1770	CLOCEXT=GDE
1771	CLOCCODE=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.code.def
1772	CLOCREST=--read-lang-def=$(ARBHOME)/SOURCE_TOOLS/arb.cloc.rest.def
1773	CLOCFILT=tail --lines=+4
1774
1775	cloc:
1776	@echo 'Arb code:'
1777	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCARB) \| $(CLOCFILT)
1778	@echo 'Arb rest:'
1779	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCARB) \| $(CLOCFILT)
1780	@echo 'External code:'
1781	@$(CLOC) $(CLOCFLAGS) $(CLOCCODE) $(CLOCEXT) \| $(CLOCFILT)
1782	@echo 'External rest:'
1783	@$(CLOC) $(CLOCFLAGS) $(CLOCREST) $(CLOCEXT) \| $(CLOCFILT)
1784
1785	# ---------------------------------------- check ressources
1786
1787	check_res:
1788	$(ARBHOME)/SOURCE_TOOLS/check_ressources.pl
1789
1790	# ---------------------------------------- cleaning
1791
1792	rmbak:
1793	@echo "Cleanup:"
1794	@find . \( -name '*%' \
1795	-o -name '*.bak' \
1796	-o -name '*~' \) \
1797	-o \( -name 'core' -a \! -type d \) \
1798	-exec rm -v {} \;
1799
1800	bin_reinit:
1801	$(MAKE) bin/bin.clean
1802	$(MAKE) -C "bin" all
1803
1804	clean_directories:
1805	-rm -rf \
1806	$(ARBHOME)/PROBE_SET/bin \
1807	$(ARBHOME)/INCLUDE \
1808
1809	libclean:
1810	-find $(ARBHOME) -type f \( -name '*.a' ! -type l \) -exec rm -f {} \;
1811
1812	objclean:
1813	-find $(ARBHOME) -type f \( -name '*.o' ! -type l \) -exec rm -f {} \;
1814
1815	# bin.clean and HELP_SOURCE.clean interfere
1816	clean3:
1817	$(MAKE) bin/bin.clean
1818	$(MAKE) HELP_SOURCE/HELP_SOURCE.clean
1819
1820	clean2: $(ARCHS:.a=.clean) \
1821	clean3 \
1822	rmbak \
1823	libclean \
1824	objclean \
1825	lib/lib.clean \
1826	GDEHELP/GDEHELP.clean \
1827	HEADERLIBS/HEADERLIBS.clean \
1828	SOURCE_TOOLS/SOURCE_TOOLS.clean \
1829	SOURCE_TOOLS/COMPILE_COMPAT/COMPILE_COMPAT.clean \
1830	UNIT_TESTER/UNIT_TESTER.clean \
1831	TEMPLATES/TEMPLATES.clean \
1832	perl_clean \
1833	clean_directories \
1834
1835	rm -f .last_gcc .last_compiler config.makefile.bak
1836
1837	# links are needed for cleanup
1838	clean: redo_links motif_xpm_hack_clean
1839	$(MAKE) clean2
1840	$(MAKE) clean_cov_all clean_links
1841
1842	silent_clean:
1843	$(MAKE) clean >/dev/null
1844
1845	# 'relocated' is about 50% faster than 'rebuild'
1846	reloc_clean: links
1847	@echo "---------------------------------------- Relocation cleanup"
1848	$(MAKE) \
1849	perl_clean \
1850	GDEHELP/GDEHELP.clean \
1851	HELP_SOURCE/genhelp/genhelp.clean \
1852	bin/bin.clean \
1853	libclean \
1854	objclean
1855
1856	relocated: links
1857	$(MAKE) reloc_clean
1858	@echo "---------------------------------------- and remake"
1859	$(MAKE) build
1860
1861	# -----------------------------------
1862	# some stress tests:
1863
1864	rebuild4ever: rebuild
1865	$(MAKE) rebuild4ever
1866
1867	build4ever: build
1868	$(MAKE) build4ever
1869
1870	clean4ever: clean
1871	$(MAKE) clean4ever
1872
1873	test4ever: ut
1874	$(MAKE) test4ever
1875
1876	perl4ever: clean
1877	$(MAKE) links
1878	$(MAKE) perl
1879	$(MAKE) perl4ever
1880
1881
1882	# -----------------------------------
1883
1884	rebuild: clean
1885	$(MAKE) all
1886
1887	relink: bin/bin.clean libclean
1888	$(MAKE) build
1889
1890	tarfile: rebuild
1891	$(MAKE) prepare_libdir
1892	util/arb_compress
1893
1894	tarfile_quick: build
1895	$(MAKE) prepare_libdir
1896	util/arb_compress
1897
1898	save: sourcetarfile
1899
1900	patch:
1901	SOURCE_TOOLS/arb_create_patch.sh arbPatch
1902
1903	# test early whether save will work
1904	savetest:
1905	@util/arb_srclst.pl >/dev/null
1906
1907	testsave: savetest
1908
1909	sourcetarfile: rmbak
1910	util/arb_save
1911
1912	save2: rmbak
1913	util/arb_save ignore
1914
1915	save_test: rmbak
1916	@echo "Testing source list.."
1917	@util/arb_srclst.pl > /dev/null
1918
1919	save_test_no_error:
1920	@-$(MAKE) save_test
1921
1922	inc_candi:
1923	touch SOURCE_TOOLS/inc_candi.stamp
1924	$(MAKE) do_version_update
1925
1926	inc_patch:
1927	touch SOURCE_TOOLS/inc_patch.stamp
1928	$(MAKE) do_version_update
1929
1930	inc_minor:
1931	touch SOURCE_TOOLS/inc_minor.stamp
1932	$(MAKE) do_version_update
1933
1934	inc_major:
1935	touch SOURCE_TOOLS/inc_major.stamp
1936	$(MAKE) do_version_update
1937
1938	do_version_update:
1939	@echo Incrementing version information
1940	$(MAKE) testsave
1941	$(MAKE) genheaders # auto upgrades version early
1942
1943	show_version:
1944	$(MAKE) genheaders # updates version info
1945	@echo "$(SEP) ARB version info"
1946	@grep ARB_VERSION TEMPLATES/arb_build.h
1947	@echo "$(SEP)"
1948
1949	release_quick:
1950	-rm arb.tgz arbsrc.tgz
1951	$(MAKE) tarfile_quick
1952	$(MAKE) sourcetarfile
1953
1954	# --------------------------------------------------------------------------------
1955
1956	MAKE_IF_COMMITTED=$(MAKE) -C SOURCE_TOOLS -f Makefile.commitbuild
1957
1958	build_CTARGET:
1959	+$(MAKE_IF_COMMITTED) "CTARGET=$(CTARGET)" build_CTARGET
1960
1961	reset_committed_build:
1962	+$(MAKE_IF_COMMITTED) reset
1963
1964	# --------------------------------------------------------------------------------
1965
1966	arbapplications: nt pa e4 wetc pt na nal di ph ds wetc cma
1967
1968	arb_external: convert tools gde readseq tg pst xmlin
1969
1970	arb_no_perl: arbapplications help arb_external
1971
1972	arb: motif_xpm_hack
1973	$(MAKE) "WITHPERL=1" perl arb_no_perl
1974
1975	motif_xpm_hack:
1976	$(MAKE) -r -C "lib/motifHack" all
1977
1978	motif_xpm_hack_clean:
1979	$(MAKE) -r -C "lib/motifHack" clean
1980
1981	# --------------------------------------------------------------------------------
1982	# special targets for SOURCE_TOOLS/remake_after_change.pl
1983
1984	rac_arb_dist: di
1985	rac_arb_edit4: e4
1986	rac_arb_ntree: nt
1987	rac_arb_pars: pa
1988	rac_arb_phylo: ph
1989	rac_arb_wetc: wetc
1990	rac_arb_naligner: nal
1991	rac_arb_pt_server: pt
1992	rac_arb_db_server: ds
1993	rac_arb_name_server: na
1994	rac_arb_convert_aln: convert
1995	rac_arb_treegen: tg
1996	rac_arb_rnacma: cma
1997	rac_arb_help2xml: help
1998
1999	rac_arb_a2ps: tools
2000	rac_arb_consensus_tree: tools
2001	rac_arb_dnarates: tools
2002	rac_arb_export_rates: tools
2003	rac_arb_export_tree: tools
2004	rac_arb_gene_probe: tools
2005	rac_arb_message: tools
2006	rac_arb_notify: tools
2007	rac_arb_primer: tools
2008	rac_arb_probe: tools
2009	rac_arb_read_tree: tools
2010
2011	# --------------------------------------------------------------------------------
2012	# unit testing
2013	# @@@ work in progress
2014	#
2015	# goal is to automatically test all libraries/executables using TESTED_UNITS_AUTO
2016	#
2017	# currently not all test executables link w/o error
2018	# (see UNITS_WORKING, UNITS_UNTESTABLE_ATM and UNITS_NEED_FIX)
2019
2020	# define RNA3D/RNA3D.test
2021	RNA3D_TEST := $(subst .a,.test,$(RNA3D_LIB))
2022
2023	TESTED_UNITS_AUTO = $(ARCHS:.a=.test)
2024
2025	UNITS_WORKING = \
2026	$(RNA3D_TEST) \
2027	AWTI/AWTI.test \
2028	DIST/DIST.test \
2029	EISPACK/EISPACK.test \
2030	GENOM/GENOM.test \
2031	GL/glAW/libglAW.test \
2032	GL/glpng/libglpng_arb.test \
2033	ISLAND_HOPPING/ISLAND_HOPPING.test \
2034	NALIGNER/NALIGNER.test \
2035	NAMES/NAMES.test \
2036	PHYLO/PHYLO.test \
2037	PRIMER_DESIGN/PRIMER_DESIGN.test \
2038	PROBE_DESIGN/PROBE_DESIGN.test \
2039	SECEDIT/SECEDIT.test \
2040	SEQ_QUALITY/SEQ_QUALITY.test \
2041	SERVERCNTRL/SERVERCNTRL.test \
2042	SL/ALIVIEW/ALIVIEW.test \
2043	SL/AP_TREE/AP_TREE.test \
2044	SL/ARB_TREE/ARB_TREE.test \
2045	SL/AW_HELIX/AW_HELIX.test \
2046	SL/AW_NAME/AW_NAME.test \
2047	SL/DB_SCANNER/DB_SCANNER.test \
2048	SL/GUI_ALIVIEW/GUI_ALIVIEW.test \
2049	SL/HELIX/HELIX.test \
2050	SL/ITEMS/ITEMS.test \
2051	SL/LOCATION/LOCATION.test \
2052	SL/MATRIX/MATRIX.test \
2053	SL/REFENTRIES/REFENTRIES.test \
2054	SL/SEQUENCE/SEQUENCE.test \
2055	SL/TRANSLATE/TRANSLATE.test \
2056	SL/TREE_ADMIN/TREE_ADMIN.test \
2057	SL/TREE_WRITE/TREE_WRITE.test \
2058	STAT/STAT.test \
2059	TREEGEN/TREEGEN.test \
2060	WETC/WETC.test \
2061	XML/XML.test \
2062	SL/ROOTED_TREE/ROOTED_TREE.test \
2063
2064	# untestable units
2065
2066	UNITS_NEED_FIX = \
2067	ptpan/PROBE.test \
2068
2069	UNITS_UNTESTABLE_ATM = \
2070	PROBE_SET/PROBE_SET.test \
2071	XML_IMPORT/XML_IMPORT.test \
2072
2073	# for the moment, put all units containing tests into UNITS_TESTED or UNITS_TESTED_FIRST
2074
2075	UNITS_TESTED_FIRST = \
2076	PARSIMONY/PARSIMONY.test \
2077	SL/NEIGHBOURJOIN/NEIGHBOURJOIN.test \
2078	SL/NDS/NDS.test \
2079	ARB_GDE/ARB_GDE.test \
2080	GENOM_IMPORT/GENOM_IMPORT.test \
2081	SL/MACROS/MACROS.test \
2082	SL/REGEXPR/REGEXPR.test \
2083	SL/FILTER/FILTER.test \
2084	ARBDB/libARBDB.test \
2085	CONSENSUS_TREE/CONSENSUS_TREE.test \
2086	TOOLS/arb_consensus_tree.test \
2087	TOOLS/arb_test.test \
2088	TOOLS/arb_probe.test \
2089	PERLTOOLS/arb_proto_2_xsub.test \
2090	AWTC/AWTC.test \
2091
2092	# plain test-libaries not linked anywhere
2093	TEST_SANDBOXES = \
2094	SL/CB/CB.test \
2095
2096	UNITS_TESTED = \
2097	SL/TREE_READ/TREE_READ.test \
2098	DBSERVER/DBSERVER.test \
2099	AWT/libAWT.test \
2100	CORE/libCORE.test \
2101	SL/INSDEL/INSDEL.test \
2102	SL/TREEDISP/TREEDISP.test \
2103	NTREE/NTREE.test \
2104	AISC_MKPTPS/mkptypes.test \
2105	EDIT4/EDIT4.test \
2106	MERGE/MERGE.test \
2107	MULTI_PROBE/MULTI_PROBE.test \
2108	SERVERCNTRL/SERVERCNTRL.test \
2109	SL/FAST_ALIGNER/FAST_ALIGNER.test \
2110	SL/PRONUC/PRONUC.test \
2111	WINDOW/libWINDOW.test \
2112	HELP_SOURCE/arb_help2xml.test \
2113	CONVERTALN/CONVERTALN.test \
2114	SL/SEQIO/SEQIO.test \
2115	SL/PTCLEAN/PTCLEAN.test \
2116	PROBE/PROBE.test \
2117	SL/DB_QUERY/DB_QUERY.test \
2118
2119	TESTED_UNITS_MANUAL = \
2120	$(TEST_SANDBOXES) \
2121	$(UNITS_TESTED_FIRST) \
2122	$(UNITS_TESTED) \
2123
2124	# $(UNITS_WORKING)
2125
2126	# see UNIT_TESTER/sym2testcode.pl@disableErrorOnUnitsWithoutTests
2127
2128	#TESTED_UNITS = $(TESTED_UNITS_AUTO)
2129	TESTED_UNITS = $(TESTED_UNITS_MANUAL)
2130
2131	# ----------------------------------------
2132
2133	TEST_LOG_DIR = UNIT_TESTER/logs
2134	TEST_RUN_SUITE=$(MAKE) $(NODIR) -C UNIT_TESTER -f Makefile.suite -r
2135	TEST_MAKE_FLAGS=
2136	TEST_POST_CLEAN=
2137	ifeq ($(COVERAGE),1)
2138	TEST_POST_CLEAN=$(MAKE) clean_cov
2139	TEST_MAKE_FLAGS+=-j1
2140	endif
2141
2142
2143	%.test:
2144	-@( export ID=$$$$; mkdir -p $(TEST_LOG_DIR); \
2145	( \
2146	echo "fake[1]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"; \
2147	$(MAKE) -C UNIT_TESTER -f Makefile.test -r \
2148	"UNITDIR=$(@D)" \
2149	"UNITLIBNAME=$(@F:.test=)" \
2150	"COVERAGE=$(COVERAGE)" \
2151	"ARB_PID=$(ARB_PID)_$(@F)" \
2152	runtest; \
2153	echo "fake[1]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"; \
2154	$(TEST_POST_CLEAN) \
2155	) >$(TEST_LOG_DIR)/$(@F).log 2>&1; \
2156	UNIT_TESTER/log_result.pl $(TEST_LOG_DIR)/$(@F).log )
2157
2158
2159	test_base: $(UNIT_TESTER_LIB:.a=.dummy) $(subst .test,.dummy,$(TEST_SANDBOXES))
2160
2161	clean_cov:
2162	find . \( -name ".gcda" -o -name ".gcov" -o -name "*.cov" \) -exec rm {} \;
2163
2164	clean_cov_all: clean_cov
2165	find . \( -name "*.gcno" \) -exec rm {} \;
2166
2167	run_tests: test_base clean_cov
2168	$(MAKE) "ARB_PID=UT_$$$$" run_tests_faked_arbpid
2169
2170	cleanup_faked_arbpids:
2171	@-rm ~/.arb_tmp/tmp/arb_pids_${USER}_${ARB_PID}_*
2172
2173	cleanup_faked_arbpids_and_fail: cleanup_faked_arbpids
2174	@false
2175
2176	run_tests_faked_arbpid:
2177	+@$(TEST_RUN_SUITE) init
2178	@echo "fake[2]: Entering directory \`$(ARBHOME)/UNIT_TESTER'"
2179	$(MAKE) $(TEST_MAKE_FLAGS) $(NODIR) $(TESTED_UNITS) \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2180	@echo "fake[2]: Leaving directory \`$(ARBHOME)/UNIT_TESTER'"
2181	+@$(TEST_RUN_SUITE) cleanup \|\| $(MAKE) cleanup_faked_arbpids_and_fail
2182	@$(MAKE) clean_cov >/dev/null
2183	@$(MAKE) cleanup_faked_arbpids
2184
2185	ut:
2186	ifeq ($(UNIT_TESTS),1)
2187	@echo $(MAKE) run_tests
2188	@$(MAKE) run_tests
2189	else
2190	@echo "Not compiled with unit tests"
2191	endif
2192
2193
2194	aut:
2195	+@$(TEST_RUN_SUITE) unskip
2196	$(MAKE) ut
2197
2198	# --------------------------------------------------------------------------------
2199
2200	TIMELOG=$(ARBHOME)/arb_time.log
2201	TIMEARGS=--append --output=$(TIMELOG) --format=" %E(%S+%U) %P [%C]"
2202	TIMECMD=$(TIME) $(TIMEARGS)
2203
2204	time_one:
2205	ifeq ($(ONE_TIMED_TARGET),)
2206	@echo "Error: You have to pass ONE_TIMED_TARGET to $@"
2207	false
2208	else
2209	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET)"
2210	@$(TIMECMD) $(MAKE) $(ONE_TIMED_TARGET)
2211	@echo "$(SEP) $(MAKE) $(ONE_TIMED_TARGET) [done]"
2212	endif
2213
2214	timed_target:
2215	ifeq ($(TIMED_TARGET),)
2216	@echo "Error: You have to pass TIMED_TARGET to $@"
2217	false
2218	else
2219	@echo "Build time:" > $(TIMELOG)
2220	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2221	@cat $(TIMELOG)
2222	@rm $(TIMELOG)
2223	endif
2224
2225	timed_target_tested:
2226	ifeq ($(TIMED_TARGET),)
2227	@echo "Error: You have to pass TIMED_TARGET to $@"
2228	false
2229	else
2230	@echo "Build time:" > $(TIMELOG)
2231	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2232	$(MAKE) "ONE_TIMED_TARGET=ut" time_one
2233	@cat $(TIMELOG)
2234	@rm $(TIMELOG)
2235	endif
2236
2237	clean_timed_target:
2238	ifeq ($(TIMED_TARGET),)
2239	@echo "Error: You have to pass TIMED_TARGET to $@"
2240	false
2241	else
2242	@echo "Build time:" > $(TIMELOG)
2243	$(MAKE) "ONE_TIMED_TARGET=clean" time_one
2244	$(MAKE) "ONE_TIMED_TARGET=$(TIMED_TARGET)" time_one
2245	@cat $(TIMELOG)
2246	@rm $(TIMELOG)
2247	endif
2248
2249	# --------------------------------------------------------------------------------
2250
2251	CHECKOUT_MODIFIED=0# set to 1 to temporarily skip test for modifications (do not check in if set to 1)
2252
2253	check_svn_does_not_contain_generated:
2254	ifeq ($(CHECKOUT_MODIFIED),0)
2255	@echo "Testing that build does not modify files in SVN"
2256	@test 0 = `svn status \| wc -l` \|\| ( \
2257	echo "The checkout is not/no longer clean:"; \
2258	svn status; \
2259	echo "- if this fails instantly, your checkout is not clean"; \
2260	echo "- if this fails after other targets, these targets modify checked in data"; \
2261	echo " (a common cause may be that depends are not up to date)"; \
2262	false)
2263	else
2264	grep -Hn 'CHECKOUT_MODIFIED' Makefile
2265	endif
2266
2267	check_svn_ignores_generated:
2268	@test 0 = `svn status \| grep '^\?' \| wc -l` \|\| ( \
2269	echo "There are svn-unignored files:"; \
2270	svn status \| grep '^\?'; \
2271	echo "(all generated files should be svn-ignored)"; \
2272	false)
2273
2274	check_svn_state: check_svn_does_not_contain_generated
2275	$(MAKE) check_svn_ignores_generated
2276	$(MAKE) savetest
2277
2278	things_that_always_should_work: depends proto
2279
2280	post_commit_check:
2281	@echo "---------------------------------------- [Initial]"
2282	$(MAKE) check_svn_state
2283
2284	$(MAKE) clean
2285	@echo "---------------------------------------- [After 'make clean']"
2286	$(MAKE) check_svn_state
2287
2288	$(MAKE) things_that_always_should_work
2289	@echo "---------------------------------------- [After 'make things_that_always_should_work']"
2290	$(MAKE) check_svn_state
2291
2292	$(MAKE) all
2293	@echo "---------------------------------------- [After 'make all']"
2294	$(MAKE) check_svn_state
2295
2296	$(MAKE) things_that_always_should_work
2297	@echo "---------------------------------------- [Final]"
2298	$(MAKE) check_svn_state
2299
2300	# --------------------------------------------------------------------------------
2301
2302	build: arb
2303	$(MAKE) binlink preplib compile_compatibility
2304
2305	all:
2306	@echo "Build time" > $(TIMELOG)
2307	@echo "$(SEP) $(MAKE) build"
2308	@$(TIMECMD) $(MAKE) build
2309	@echo $(SEP)
2310	@echo "made 'all' with success."
2311	@echo "to start arb enter 'arb'"
2312	ifeq ($(UNIT_TESTS),1)
2313	@echo $(MAKE) run_tests
2314	@$(TIMECMD) $(MAKE) run_tests
2315	endif
2316	@echo "$(SEP) $(MAKE) build [done]"
2317	@$(MAKE) save_test_no_error >/dev/null # just show hints
2318	@cat $(TIMELOG)
2319	@rm $(TIMELOG)
2320

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